Multiple sequence alignment - TraesCS6A01G171600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G171600 chr6A 100.000 2722 0 0 1 2722 182420390 182417669 0.000000e+00 5027
1 TraesCS6A01G171600 chr6A 94.263 1377 52 9 1 1370 137493489 137492133 0.000000e+00 2080
2 TraesCS6A01G171600 chr6A 92.593 1404 60 19 1354 2720 137393776 137392380 0.000000e+00 1977
3 TraesCS6A01G171600 chr2A 95.719 2733 82 12 1 2722 778648759 778651467 0.000000e+00 4366
4 TraesCS6A01G171600 chr3B 95.108 2412 84 12 1 2384 473235657 473238062 0.000000e+00 3770
5 TraesCS6A01G171600 chr3B 84.766 1431 170 28 3 1390 766341705 766343130 0.000000e+00 1391
6 TraesCS6A01G171600 chr3B 90.716 517 38 10 2212 2722 473237924 473238436 0.000000e+00 680
7 TraesCS6A01G171600 chr7A 94.985 2393 92 11 1 2384 126148516 126150889 0.000000e+00 3729
8 TraesCS6A01G171600 chr7A 88.824 510 45 10 2217 2720 126150757 126151260 1.390000e-172 616
9 TraesCS6A01G171600 chr7B 94.615 2414 97 12 1 2384 51883772 51886182 0.000000e+00 3707
10 TraesCS6A01G171600 chr7B 84.916 1432 167 29 3 1390 73167738 73169164 0.000000e+00 1402
11 TraesCS6A01G171600 chr7B 90.329 517 42 8 2211 2722 51886043 51886556 0.000000e+00 671
12 TraesCS6A01G171600 chr6B 94.279 2412 95 12 1 2384 48079468 48081864 0.000000e+00 3650
13 TraesCS6A01G171600 chr6B 89.555 517 46 8 2211 2722 48081725 48082238 0.000000e+00 649
14 TraesCS6A01G171600 chr4B 93.903 2411 116 12 1 2384 321542005 321544411 0.000000e+00 3609
15 TraesCS6A01G171600 chr4B 93.730 1595 74 8 813 2384 587099150 587100741 0.000000e+00 2368
16 TraesCS6A01G171600 chr4B 95.269 782 29 6 1 776 587098368 587099147 0.000000e+00 1232
17 TraesCS6A01G171600 chr4B 90.504 516 40 9 2211 2722 587100604 587101114 0.000000e+00 673
18 TraesCS6A01G171600 chr4B 89.655 522 35 14 2212 2722 321544273 321544786 0.000000e+00 647
19 TraesCS6A01G171600 chr5A 82.310 2199 297 48 198 2337 514149474 514147309 0.000000e+00 1821
20 TraesCS6A01G171600 chr3A 95.755 848 30 4 1 843 153362652 153363498 0.000000e+00 1362
21 TraesCS6A01G171600 chr3A 92.973 370 20 4 2352 2720 644687576 644687212 3.990000e-148 534
22 TraesCS6A01G171600 chr6D 90.249 482 41 6 2243 2722 16251830 16252307 2.300000e-175 625


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G171600 chr6A 182417669 182420390 2721 True 5027.000000 5027 100.000000 1 2722 1 chr6A.!!$R3 2721
1 TraesCS6A01G171600 chr6A 137492133 137493489 1356 True 2080.000000 2080 94.263000 1 1370 1 chr6A.!!$R2 1369
2 TraesCS6A01G171600 chr6A 137392380 137393776 1396 True 1977.000000 1977 92.593000 1354 2720 1 chr6A.!!$R1 1366
3 TraesCS6A01G171600 chr2A 778648759 778651467 2708 False 4366.000000 4366 95.719000 1 2722 1 chr2A.!!$F1 2721
4 TraesCS6A01G171600 chr3B 473235657 473238436 2779 False 2225.000000 3770 92.912000 1 2722 2 chr3B.!!$F2 2721
5 TraesCS6A01G171600 chr3B 766341705 766343130 1425 False 1391.000000 1391 84.766000 3 1390 1 chr3B.!!$F1 1387
6 TraesCS6A01G171600 chr7A 126148516 126151260 2744 False 2172.500000 3729 91.904500 1 2720 2 chr7A.!!$F1 2719
7 TraesCS6A01G171600 chr7B 51883772 51886556 2784 False 2189.000000 3707 92.472000 1 2722 2 chr7B.!!$F2 2721
8 TraesCS6A01G171600 chr7B 73167738 73169164 1426 False 1402.000000 1402 84.916000 3 1390 1 chr7B.!!$F1 1387
9 TraesCS6A01G171600 chr6B 48079468 48082238 2770 False 2149.500000 3650 91.917000 1 2722 2 chr6B.!!$F1 2721
10 TraesCS6A01G171600 chr4B 321542005 321544786 2781 False 2128.000000 3609 91.779000 1 2722 2 chr4B.!!$F1 2721
11 TraesCS6A01G171600 chr4B 587098368 587101114 2746 False 1424.333333 2368 93.167667 1 2722 3 chr4B.!!$F2 2721
12 TraesCS6A01G171600 chr5A 514147309 514149474 2165 True 1821.000000 1821 82.310000 198 2337 1 chr5A.!!$R1 2139
13 TraesCS6A01G171600 chr3A 153362652 153363498 846 False 1362.000000 1362 95.755000 1 843 1 chr3A.!!$F1 842

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
254 264 1.354101 TACCGATCAAGGTTGGGTGT 58.646 50.0 0.0 0.0 43.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2138 0.178301 GCTCCCGGTAAAGCTAAGCT 59.822 55.0 12.15 0.0 42.56 3.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.397103 TGAAGCTTCATCCATTGCTACTTG 59.603 41.667 25.16 0.00 35.09 3.16
179 189 9.944663 GTTGTTTATGTTGTAGAATTGTCTTGA 57.055 29.630 0.00 0.00 35.12 3.02
254 264 1.354101 TACCGATCAAGGTTGGGTGT 58.646 50.000 0.00 0.00 43.00 4.16
282 294 3.708563 ACAAATGTGTTAGGTGTGTGC 57.291 42.857 0.00 0.00 32.58 4.57
482 495 5.068591 GTCAAAAGTATCACTTGGGTGGTTT 59.931 40.000 0.00 0.00 43.17 3.27
566 579 7.554476 AGCCTGAAATATTGTAGAAAGGTCTTC 59.446 37.037 0.00 0.00 35.12 2.87
799 828 2.135664 ACTTCGAACGAGTGGACAAG 57.864 50.000 0.00 0.00 0.00 3.16
1397 1487 4.095410 TCCTTGTTAATGCTGAATTGCG 57.905 40.909 0.00 0.00 35.36 4.85
1400 1490 3.913548 TGTTAATGCTGAATTGCGTGT 57.086 38.095 0.00 0.00 35.36 4.49
1472 1580 3.007635 CGGAAGATGTTGTACCTTTCCC 58.992 50.000 0.00 0.00 0.00 3.97
1522 1641 6.508777 TCGTTGCCTTTTTGTATAGCTTTTT 58.491 32.000 0.00 0.00 0.00 1.94
1685 1805 1.151668 CTGAAGGCTTTGGTGAGACG 58.848 55.000 0.00 0.00 0.00 4.18
1759 1879 3.454082 GAGGACTTGATCTCAACAGGGAT 59.546 47.826 0.00 0.00 0.00 3.85
1897 2017 3.472283 AGATGTCAATAGCCAGCTGAG 57.528 47.619 17.39 6.56 0.00 3.35
2039 2160 1.068741 CTTAGCTTTACCGGGAGCGAT 59.931 52.381 17.43 7.21 43.53 4.58
2043 2164 1.272769 GCTTTACCGGGAGCGATATCT 59.727 52.381 6.32 0.00 0.00 1.98
2050 2171 1.341531 CGGGAGCGATATCTTTGAGGT 59.658 52.381 0.34 0.00 0.00 3.85
2055 2176 3.201290 AGCGATATCTTTGAGGTTGCAG 58.799 45.455 0.34 0.00 0.00 4.41
2087 2208 4.751098 GCTAAAGCTCCAGATCAGATGAAG 59.249 45.833 0.00 0.00 38.21 3.02
2233 2368 3.897505 TCTGATTGGCTAGCTGCTATACA 59.102 43.478 15.72 9.34 42.39 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.703052 TCGGGTATAGGTTCTGGTTTCTC 59.297 47.826 0.00 0.00 0.00 2.87
179 189 1.156736 GTGTGTGCCATCTAACGCTT 58.843 50.000 0.00 0.00 0.00 4.68
282 294 1.229975 TGAACTGCATGTCAGGTGCG 61.230 55.000 17.61 0.00 44.28 5.34
370 383 1.265236 GGGACATGCAACCCATTTGA 58.735 50.000 18.12 0.00 44.96 2.69
482 495 1.148273 GGTGGGTTCTGTGCTGTCA 59.852 57.895 0.00 0.00 0.00 3.58
566 579 1.204941 CACTGACCCTTAGTCTTCCGG 59.795 57.143 0.00 0.00 46.46 5.14
618 636 4.014569 TGATTCGACATTGGGTCTTCAA 57.985 40.909 0.00 0.00 44.68 2.69
799 828 1.963747 CGCAAGAACATTCCGGAAAC 58.036 50.000 23.08 12.81 43.02 2.78
971 1033 9.248291 CTGTACAAAGCAAGAACAAATACAAAT 57.752 29.630 0.00 0.00 0.00 2.32
972 1034 8.462811 TCTGTACAAAGCAAGAACAAATACAAA 58.537 29.630 0.00 0.00 0.00 2.83
973 1035 7.990917 TCTGTACAAAGCAAGAACAAATACAA 58.009 30.769 0.00 0.00 0.00 2.41
974 1036 7.561021 TCTGTACAAAGCAAGAACAAATACA 57.439 32.000 0.00 0.00 0.00 2.29
977 1039 8.246180 CCATATCTGTACAAAGCAAGAACAAAT 58.754 33.333 0.00 0.00 0.00 2.32
978 1040 7.446931 TCCATATCTGTACAAAGCAAGAACAAA 59.553 33.333 0.00 0.00 0.00 2.83
1397 1487 8.079809 ACTACAATAACAATAACAAGGCAACAC 58.920 33.333 0.00 0.00 41.41 3.32
1400 1490 8.172352 ACACTACAATAACAATAACAAGGCAA 57.828 30.769 0.00 0.00 0.00 4.52
1522 1641 8.830915 AGGAACTTAGTCTCTGATAGAAATGA 57.169 34.615 0.00 0.00 31.04 2.57
1685 1805 4.681074 TTCATTTTCCAAGTTTCCCACC 57.319 40.909 0.00 0.00 0.00 4.61
1719 1839 4.712337 GTCCTCTTCCTCATGTTCCTCTTA 59.288 45.833 0.00 0.00 0.00 2.10
1759 1879 2.616634 ATCGACAGACCGTCTAGCTA 57.383 50.000 0.00 0.00 42.98 3.32
1897 2017 3.193267 ACCCACATATTGTGTCACATTGC 59.807 43.478 6.48 0.00 46.45 3.56
2017 2138 0.178301 GCTCCCGGTAAAGCTAAGCT 59.822 55.000 12.15 0.00 42.56 3.74
2039 2160 2.877097 TGGCTGCAACCTCAAAGATA 57.123 45.000 7.82 0.00 0.00 1.98
2043 2164 3.617045 GCAAATATGGCTGCAACCTCAAA 60.617 43.478 7.82 0.00 38.48 2.69
2050 2171 3.448301 AGCTTTAGCAAATATGGCTGCAA 59.552 39.130 11.36 0.00 45.16 4.08
2055 2176 3.885297 TCTGGAGCTTTAGCAAATATGGC 59.115 43.478 4.33 0.00 45.16 4.40
2087 2208 1.146637 CTAGAAGCGCAGGCATCATC 58.853 55.000 11.47 0.00 43.41 2.92
2233 2368 8.217799 AGCTAGTCAAGTAGAGATTACAGATCT 58.782 37.037 0.00 0.00 0.00 2.75


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.